[Bioperl-l] tracking down error in SeqFeature Collection subroutine

[Robson Francisco de Souza]

On Fri, 21 Feb 2003, Andy Nunberg wrote:
> Hi,
[snip]
> I dont see _compare being explicitly called in add_features.  So when is it
> called, if ever , in the add_features subroutine?
> the line of code in question is this
> 
> my $nof_added = $self->{'_sfc'}->add_features($args);
> 
> I am pretty sure that $self->{'_sfc'} is accessing the objects SeqFeature
> Collection object(Robson is that correct?).

	Yes. $self->{'_sfc'} is a reference to a
Bio::SeqFeature::Collection in Bio::Assembly::Contig objects. 

> the warning i am getting is the following
> Argument "" isn't numeric in numeric comparison (<=>) at
> /loginhome/anunberg/bioperl-1.2/Bio/SeqFeature/Collection.pm line 436,

	I guess, somehow, ace.pm is loosing some data while adding read
features to the contig feature collection, but I could not reproduce
Andy's error messages.
	Jason: does Bio::SeqFeature::Collection uses _compare while
adding features? Wouldn't it throw these messages if features were missing
start or end coordinates?
					Robson

> Thanks
> Andy
> *******************************************************************
> Andy Nunberg, Ph.D
> Computational Biologist
> Orion Genomics, LLC 
> (314) 615-6989
> http://www.oriongenomics.com
> 
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